Whether a body rotates clockwise or counter clockwise depends on your position relative to the body. An observer located above one pole sees the body rotating in the sense opposite to that observed by an observer located above the other pole.

Venus rotates in a sense opposite to all other bodies in the solar system.

Current theories suggest that most bodies in our solar system condensed out of a protoplanetary disk, which would have developed an axis of rotation which was an average of the angular momentum of matter in that part of the dust cloud.

This would have resulted in the Sun, most planets and most moons rotating in the same direction, in roughly the same plane.

Various gravitational interactions between planets - plus direct collisions - can result in planets and planetoids being thrown into orbits with different inclinations, and becoming tidally locked, which would disguise some of the original chaotic patterns in the protoplanetary disk.

However, bodies which were outside the protoplanetary disk, such as Kuiper Belt objects, and objects from the Oort cloud (which includes todays comets) would have a more spherical distribution, and could approach in any direction. If these were captured by a planet as a moon, they could take on any orbit, including retrograde orbits.

As for the origin of "clockwise", I understand that early clockmakers in the Northern Hemisphere designed the position of the numbers on the clock face to imitate the numbers on a sundial. However, sundials in the Southern Hemisphere are built facing the opposite direction (ie facing the equator=North), and have the numbers inscribed in the opposite direction.